Rosetta 3.4
Public Types | Public Member Functions
protocols::anchored_design::AnchorMoversData Class Reference

This data class wraps all the data needed for the AnchoredDesign movers. More...

#include <AnchorMoversData.hh>

Inheritance diagram for protocols::anchored_design::AnchorMoversData:
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List of all members.

Public Types

typedef
utility::keys::Key3Tuple
< protocols::loops::Loop,
core::kinematics::MoveMapOP,
core::kinematics::MoveMapOP
Loop_mm_tuple
typedef utility::vector1
< Loop_mm_tuple
Loop_mm_tuples

Public Member Functions

 AnchorMoversData ()
 empty constructor is empty - don't use it unless you intend to set alllllllll the data manually...
 AnchorMoversData (protocols::anchored_design::AnchorCOP anchor, protocols::loops::Loops const &loops, bool const options=false)
 constructor takes an anchor and loop object and sets up internals reasonably; options boolean is optionally optional. If you use this constructor, you will need to later manually give fragments to the AnchorMoversData object or use one of its fragments functions to determine what type of fragments to use.
 AnchorMoversData (core::pose::Pose const &pose)
 constructor takes a pose to generate its own internals (also using the option system)
virtual ~AnchorMoversData ()
 virtual dtors make c++ happy
 AnchorMoversData (AnchorMoversData const &rhs)
 copy ctor
AnchorMoversDataoperator= (AnchorMoversData const &rhs)
 assignment operator
AnchorMoversDataOP clone () const
void pick_new_cutpoints (bool reset_always)
 randomly reset loop cutpoints. Useful only when starting structure is well-closed. Best for MPI-style runs
void anchor_noise_constraints_setup (core::pose::Pose &pose)
 set up constraints for anchor_noise_constraints_mode
void set_frags (core::fragment::FragSetOP)
 set fragments object
core::fragment::FragSetCOP autogenerate_design_frags ()
 brew its own design frags (LLLLL secondary structure)
core::fragment::FragSetCOP autogenerate_constseq_frags (std::string const &seq)
 brew its own sequence-specific frags
void autogenerate_frags (core::pose::Pose const &pose)
 figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring
void set_task_factory (core::pack::task::TaskFactoryOP)
 set packertask factory
void set_fullatom_scorefunction (core::scoring::ScoreFunctionOP)
 set fullatom scorefunction
void set_centroid_scorefunction (core::scoring::ScoreFunctionOP)
 set centroid scorefunction
void set_loops_and_anchor (protocols::anchored_design::AnchorCOP anchor, protocols::loops::Loops loops)
 set up kinematics' loops and anchors
protocols::loops::Loop const & anchored_loop () const
 access anchored loop
core::kinematics::MoveMapOP movemap_fa_all () const
 access for movemap that covers all loops; fullatom
core::kinematics::MoveMapOP movemap_cen_all () const
 access for movemap that covers all loops; centroid
core::Size num_loops () const
 number of loops/mms
protocols::loops::Loop const & loop (core::Size i) const
 accessor for a loop
core::kinematics::MoveMapOP movemap_fa (core::Size i) const
 accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints)
core::kinematics::MoveMapOP movemap_fa_omegafixed (core::Size i) const
 accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints)
core::kinematics::MoveMapOP movemap_cen (core::Size i) const
 accessor for omega-variable movemap (most movers); centroid phase (no anchor movement)
core::kinematics::MoveMapOP movemap_cen_omegafixed (core::Size i) const
 accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase
protocols::loops::Loops const & loops () const
 accessor for loops object
core::Size anchor_start () const
 access for anchor start
core::Size anchor_end () const
 access for anchor end
core::fragment::FragSetCOP get_frags () const
 access fragments object
core::pack::task::TaskFactoryCOP get_task_factory () const
 access packertask factory
core::pack::task::TaskFactoryCOP get_late_factory () const
 access packertask factory
core::scoring::ScoreFunctionOP get_fullatom_scorefunction () const
 access fullatom scorefunction
core::scoring::ScoreFunctionOP get_centroid_scorefunction () const
 access centroid scorefunction
core::scoring::ScoreFunctionOP get_centroid_scorefunction_min () const
 access centroid scorefunction for minimization
core::pack::task::PackerTaskOP get_task (core::pose::Pose const &pose) const
 return packertask from factory
void set_akash_dyepos (core::Size const akash_dyepos)
 dye position used in dye modeling publication
void set_unbound_mode (bool unbound_mode)
 used for unbound mode
void set_anchor_via_constraints (bool anchor_via_constraints)
 used to test anchoring via constraints
void set_VDW_weight (core::Real VDW_weight)
 VDW weight in centroid scorefunction.
void set_chainbreak_weight (core::Real chainbreak_weight)
 chainbreak weight in fullatom scorefunction
void set_allow_anchor_repack (bool allow_anchor_repack)
 allow anchor to repack
void set_resfile_1 (std::string const &resfile_1)
 resfile for design
void set_resfile_2 (std::string const &resfile_2)
 later-stage resfile if desired
void set_frag3 (std::string const &frag3)
 copy of cmdline option loop_file
void set_no_frags (bool no_frags)
 do not use fragments?
void set_anchor_noise_constraints_mode (bool anchor_noise_constraints_mode)
 special anchor_noise_constraints_mode
core::Size get_akash_dyepos () const
 dye position used in dye modeling publication
bool get_unbound_mode () const
 used for unbound mode
bool get_anchor_via_constraints () const
 used to test anchoring via constraints
core::Real get_VDW_weight () const
 VDW weight in centroid scorefunction.
core::Real get_chainbreak_weight () const
 chainbreak weight in fullatom scorefunction
bool get_allow_anchor_repack () const
 allow anchor to repack
std::string const & get_resfile_1 () const
 resfile for design
std::string const & get_resfile_2 () const
 later-stage resfile if desired
std::string const & get_loop_file () const
 copy of cmdline option loop_file
std::string const & get_frag3 () const
 copy of cmdline option frag3
bool get_no_frags () const
 do not use fragments?
bool get_anchor_noise_constraints_mode () const
 special anchor_noise_constraints_mode
void read_options ()
 read options from the option system
std::string const & interface_calc () const
 get string name for interface_calc_
std::string const & neighborhood_calc () const
 get string name for neighborhood_calc_

Detailed Description

This data class wraps all the data needed for the AnchoredDesign movers.

This data class keeps the anchor, mobile loops, and movemaps associated with the loops all together. It generates its own movemaps.


Member Typedef Documentation


Constructor & Destructor Documentation

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( )

empty constructor is empty - don't use it unless you intend to set alllllllll the data manually...

empty, useless ctor. You'll need to manually set all the data later. Why did you make me waste my time writing this ctor?

mechanicals (ctor, dtor, etc)/////////////////////////////////////

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( protocols::anchored_design::AnchorCOP  anchor,
protocols::loops::Loops const &  loops,
bool const  options = false 
)

constructor takes an anchor and loop object and sets up internals reasonably; options boolean is optionally optional. If you use this constructor, you will need to later manually give fragments to the AnchorMoversData object or use one of its fragments functions to determine what type of fragments to use.

References read_options(), and set_loops_and_anchor().

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( core::pose::Pose const &  pose)

constructor takes a pose to generate its own internals (also using the option system)

use pose and option system to set up loops and create anchor, then call set_loops_and_anchor and set_unset_defaults to set up internal data to reasonable defaults, with or without option system help

References autogenerate_frags(), read_options(), and set_loops_and_anchor().

protocols::anchored_design::AnchorMoversData::~AnchorMoversData ( ) [virtual]

virtual dtors make c++ happy

protocols::anchored_design::AnchorMoversData::AnchorMoversData ( AnchorMoversData const &  rhs)

copy ctor


Member Function Documentation

core::Size protocols::anchored_design::AnchorMoversData::anchor_end ( ) const

access for anchor end

void protocols::anchored_design::AnchorMoversData::anchor_noise_constraints_setup ( core::pose::Pose pose)

set up constraints for anchor_noise_constraints_mode

This function automatically generates constraints for an anchor from and for the given pose. It is intended for use only with single-residue anchors. The constraints are between the residue CA and the four closest cross-chain CA. They are parabolic constraints with scores of 0.5 units at 1 Angstrom deviation.

References core::pose::Pose::add_constraint(), core::scoring::atom_pair_constraint, protocols::frag_picker::CA, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::sequence::end, core::conformation::Conformation::num_chains(), core::pose::Pose::residue_type(), protocols::TR(), and core::pose::Pose::xyz().

core::Size protocols::anchored_design::AnchorMoversData::anchor_start ( ) const

access for anchor start

anchor functions//////////////////////////////////////////////

anchor functions//////////////////////////////////////////////

access for anchor start

protocols::loops::Loop const & protocols::anchored_design::AnchorMoversData::anchored_loop ( ) const

access anchored loop

loops and movemap functions//////////////////////////////////////////////

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::autogenerate_constseq_frags ( std::string const &  seq)

brew its own sequence-specific frags

autogenerate_constseq_frags will use Andrew Ban's fragment picker to read the Vall and find fragments. It looks for fragments of loop secondary structure and known, fixed sequence. The string argument is the whole pose sequence.

References core::sequence::end, core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), and protocols::TR().

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::autogenerate_design_frags ( )

brew its own design frags (LLLLL secondary structure)

autogenerate_design_frags will use Andrew Ban's fragment picker to read the Vall and find fragments. It looks for fragments of loop secondary structure (for now, just 3mers.). This function is used in a design context and thus uses only secondary structure to define the fragments.

References core::sequence::end, core::fragment::picking_old::FragmentLibraryManager::get_instance(), core::fragment::picking_old::vall::pick_fragments_by_ss(), and protocols::TR().

void protocols::anchored_design::AnchorMoversData::autogenerate_frags ( core::pose::Pose const &  pose)

figure out what type of fragments to use, and use them; pose needed to make packertask to detect if design is occuring

autogenerate_frags will determine from this object's state what fragments to use, and generate fragments as needed. The logic was originally at the executeable level, src/apps/pilot/smlewis/AnchoredDesign.cc:116-136 SVN 40529

References protocols::anchored_design::EMPTY_STRING(), core::pose::Pose::sequence(), and protocols::TR().

Referenced by AnchorMoversData().

protocols::anchored_design::AnchorMoversDataOP protocols::anchored_design::AnchorMoversData::clone ( ) const
core::Size protocols::anchored_design::AnchorMoversData::get_akash_dyepos ( ) const

dye position used in dye modeling publication

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_allow_anchor_repack ( ) const

allow anchor to repack

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_anchor_noise_constraints_mode ( ) const

special anchor_noise_constraints_mode

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_anchor_via_constraints ( ) const

used to test anchoring via constraints

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction ( ) const

access centroid scorefunction

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_centroid_scorefunction_min ( ) const

access centroid scorefunction for minimization

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::get_chainbreak_weight ( ) const

chainbreak weight in fullatom scorefunction

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_frag3 ( ) const

copy of cmdline option frag3

frag3 file

Referenced by operator=().

core::fragment::FragSetCOP protocols::anchored_design::AnchorMoversData::get_frags ( ) const

access fragments object

scfxn, packertask, fragments accessors//////////////////////////////

Referenced by operator=().

core::scoring::ScoreFunctionOP protocols::anchored_design::AnchorMoversData::get_fullatom_scorefunction ( ) const

access fullatom scorefunction

Referenced by operator=().

core::pack::task::TaskFactoryCOP protocols::anchored_design::AnchorMoversData::get_late_factory ( ) const

access packertask factory

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_loop_file ( ) const

copy of cmdline option loop_file

loop file

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_no_frags ( ) const

do not use fragments?

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_resfile_1 ( ) const

resfile for design

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::get_resfile_2 ( ) const

later-stage resfile if desired

Referenced by operator=().

core::pack::task::PackerTaskOP protocols::anchored_design::AnchorMoversData::get_task ( core::pose::Pose const &  pose) const

return packertask from factory

runs the member factory to create a task

core::pack::task::TaskFactoryCOP protocols::anchored_design::AnchorMoversData::get_task_factory ( ) const

access packertask factory

Referenced by operator=().

bool protocols::anchored_design::AnchorMoversData::get_unbound_mode ( ) const

used for unbound mode

Referenced by operator=().

core::Real protocols::anchored_design::AnchorMoversData::get_VDW_weight ( ) const

VDW weight in centroid scorefunction.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchorMoversData::interface_calc ( ) const

get string name for interface_calc_

protocols::loops::Loop const & protocols::anchored_design::AnchorMoversData::loop ( core::Size  i) const

accessor for a loop

protocols::loops::Loops const & protocols::anchored_design::AnchorMoversData::loops ( ) const

accessor for loops object

Referenced by operator=().

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen ( core::Size  i) const

accessor for omega-variable movemap (most movers); centroid phase (no anchor movement)

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen_all ( ) const

access for movemap that covers all loops; centroid

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_cen_omegafixed ( core::Size  i) const

accessor for omega-fixed movemap (appropriate for CCD movers); centroid phase

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa ( core::Size  i) const

accessor for omega-variable movemap (most movers); fullatom phase (may allow anchor movement w/constraints)

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa_all ( ) const

access for movemap that covers all loops; fullatom

core::kinematics::MoveMapOP protocols::anchored_design::AnchorMoversData::movemap_fa_omegafixed ( core::Size  i) const

accessor for omega-fixed movemap (appropriate for CCD movers); fullatom phase (may allow anchor movement w/constraints)

std::string const & protocols::anchored_design::AnchorMoversData::neighborhood_calc ( ) const

get string name for neighborhood_calc_

core::Size protocols::anchored_design::AnchorMoversData::num_loops ( ) const [inline]

number of loops/mms

AnchorMoversData & protocols::anchored_design::AnchorMoversData::operator= ( AnchorMoversData const &  rhs)
void protocols::anchored_design::AnchorMoversData::pick_new_cutpoints ( bool  reset_always)

randomly reset loop cutpoints. Useful only when starting structure is well-closed. Best for MPI-style runs

References protocols::TR().

void protocols::anchored_design::AnchorMoversData::read_options ( )

read options from the option system

References protocols::anchored_design::EMPTY_STRING(), and protocols::TR().

Referenced by AnchorMoversData().

void protocols::anchored_design::AnchorMoversData::set_akash_dyepos ( core::Size const  akash_dyepos)

dye position used in dye modeling publication

option system replacement/////////////////////////////

void protocols::anchored_design::AnchorMoversData::set_allow_anchor_repack ( bool  allow_anchor_repack)

allow anchor to repack

void protocols::anchored_design::AnchorMoversData::set_anchor_noise_constraints_mode ( bool  anchor_noise_constraints_mode)

special anchor_noise_constraints_mode

void protocols::anchored_design::AnchorMoversData::set_anchor_via_constraints ( bool  anchor_via_constraints)

used to test anchoring via constraints

void protocols::anchored_design::AnchorMoversData::set_centroid_scorefunction ( core::scoring::ScoreFunctionOP  in)

set centroid scorefunction

void protocols::anchored_design::AnchorMoversData::set_chainbreak_weight ( core::Real  chainbreak_weight)

chainbreak weight in fullatom scorefunction

void protocols::anchored_design::AnchorMoversData::set_frag3 ( std::string const &  frag3)

copy of cmdline option loop_file

copy of cmdline option frag3

loop file

void protocols::anchored_design::AnchorMoversData::set_frags ( core::fragment::FragSetOP  in)

set fragments object

set functions/////////////////////////////////////////////////////////

void protocols::anchored_design::AnchorMoversData::set_fullatom_scorefunction ( core::scoring::ScoreFunctionOP  in)

set fullatom scorefunction

void protocols::anchored_design::AnchorMoversData::set_loops_and_anchor ( protocols::anchored_design::AnchorCOP  anchor,
protocols::loops::Loops  loops 
)

set up kinematics' loops and anchors

set up kinematics' loops and anchors; these are combined because loop setup depends on anchor

References protocols::loops::Loops::sequential_order().

Referenced by AnchorMoversData(), and operator=().

void protocols::anchored_design::AnchorMoversData::set_no_frags ( bool  no_frags)

do not use fragments?

void protocols::anchored_design::AnchorMoversData::set_resfile_1 ( std::string const &  resfile_1)

resfile for design

void protocols::anchored_design::AnchorMoversData::set_resfile_2 ( std::string const &  resfile_2)

later-stage resfile if desired

void protocols::anchored_design::AnchorMoversData::set_task_factory ( core::pack::task::TaskFactoryOP  in)

set packertask factory

void protocols::anchored_design::AnchorMoversData::set_unbound_mode ( bool  unbound_mode)

used for unbound mode

void protocols::anchored_design::AnchorMoversData::set_VDW_weight ( core::Real  VDW_weight)

VDW weight in centroid scorefunction.


The documentation for this class was generated from the following files:
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